diff plot.xml @ 2:c520f64ffd57 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat commit 0c7884b059c6a12ecf22a025317f04c160962be7

--- a/plot.xml	Tue Nov 05 11:55:07 2024 +0000
+++ b/plot.xml	Thu Mar 26 11:15:58 2026 +0000
@@ -6,6 +6,7 @@
     <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <expand macro="version_command"/>
+    <expand macro="creators"/>
     <command detect_errors="exit_code"><![CDATA[
 @CMD@
     ]]></command>
@@ -246,6 +247,115 @@
     combine = TRUE
 )
 
+#else if $method.method == 'ImageDimPlot'
+
+#if $method.adv.cells
+    cells_list<-paste(readLines('$method.adv.cells'), collapse=",")
+    #end if
+
+plot<-ImageDimPlot(
+    seurat_obj,
+    #if $method.plot.fov != ''
+    fov = c(unlist(strsplit(gsub(" ", "", '$method.plot.fov'), ","))),
+    #end if
+    #if $method.plot.boundaries != ''
+    boundaries = c(unlist(strsplit(gsub(" ", "", '$method.plot.boundaries'), ","))),
+    #end if
+    #if $method.adv.group_by != ''
+    group.by = '$method.adv.group_by',
+    #end if
+    #if $method.adv.split_by != ''
+    split.by = '$method.adv.split_by',
+    #end if
+    #if $method.plot.cols != ''
+    cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.cols'), ","))),
+    shuffle.cols = $method.plot.shuffle_cols,
+    #end if
+    size = $method.plot.size,
+    #if $method.plot.molecules != ''
+    molecules = c(unlist(strsplit(gsub(" ", "", '$method.plot.molecules'), ","))),
+    mols.size = $method.plot.mols_size,
+    mols.cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.mols_cols'), ","))),
+    mols.alpha = $method.plot.mols_alpha,
+    nmols = $method.plot.nmols,
+    #end if
+    alpha = $method.plot.alpha,
+    #if $method.adv.border_color != ''
+    border.color = '$method.adv.border_color',
+    #end if
+    #if $method.adv.border_size != ''
+    border.size = $method.adv.border_size,
+    #end if
+    na.value = '$method.plot.na_value',
+    dark.background = $method.adv.dark_background,
+    crop = $method.adv.crop,
+    #if $method.adv.cells
+    cells = c(unlist(strsplit(cells_list, ","))),
+    #end if
+    overlap = $method.adv.overlap,
+    axes = $method.adv.axes,
+    combine = TRUE,
+    coord.fixed = $method.adv.coord_fixed,
+    flip_xy = $method.adv.flip_xy
+)
+
+#else if $method.method == 'ImageFeaturePlot'
+
+#if $method.adv.cells
+    cells_list<-paste(readLines('$method.adv.cells'), collapse=",")
+    #end if
+
+plot<-ImageFeaturePlot(
+    seurat_obj,
+    features = '$method.features',
+    #if $method.plot.fov != ''
+    fov = c(unlist(strsplit(gsub(" ", "", '$method.plot.fov'), ","))),
+    #end if
+    #if $method.plot.boundaries != ''
+    boundaries = c(unlist(strsplit(gsub(" ", "", '$method.plot.boundaries'), ","))),
+    #end if
+    size = $method.plot.size,
+    #if $method.adv.min_cutoff != ''
+    min.cutoff = '$method.adv.min_cutoff',
+    #end if
+    #if $method.adv.max_cutoff != ''
+    max.cutoff = '$method.adv.max_cutoff',
+    #end if
+    #if $method.adv.split_by != ''
+    split.by = '$method.adv.split_by',
+    #end if
+    #if $method.plot.molecules != ''
+    molecules = c(unlist(strsplit(gsub(" ", "", '$method.plot.molecules'), ","))),
+    mols.size = $method.plot.mols_size,
+    mols.cols = c(unlist(strsplit(gsub(" ", "", '$method.plot.mols_cols'), ","))),
+    nmols = $method.plot.nmols,
+    #end if
+    alpha = $method.plot.alpha,
+    #if $method.adv.border_color != ''
+    border.color = '$method.adv.border_color',
+    #end if
+    #if $method.adv.border_size != ''
+    border.size = $method.adv.border_size,
+    #end if
+    dark.background = $method.adv.dark_background,
+    blend = $method.plot.blend,
+    #if $method.plot.blend == 'TRUE'
+    cols = c("#ff0000", "#00ff00"),
+    blend.threshold = $method.plot.blend_threshold,
+    #else
+    cols = c("lightgrey", "firebrick1"),
+    scale = '$method.plot.scale',
+    #end if
+    crop = $method.adv.crop,
+    #if $method.adv.cells
+    cells = c(unlist(strsplit(cells_list, ","))),
+    #end if
+    overlap = $method.adv.overlap,
+    axes = $method.adv.axes,
+    combine = TRUE,
+    coord.fixed = $method.adv.coord_fixed
+)
+
 #else if $method.method == 'DimHeatmap'
 plot<-DimHeatmap(
     seurat_obj,
@@ -310,8 +420,12 @@
     #end if
     alpha = $method.plot.alpha,
     order = $method.plot.order,
+    #if $method.adv.min_cutoff != ''
     min.cutoff = 'q$method.adv.min_cutoff',
+    #end if
+    #if $method.adv.max_cutoff != ''
     max.cutoff = 'q$method.adv.max_cutoff',
+    #end if
     #if $method.adv.split_by != ''
     split.by = '$method.adv.split_by',
     by.col = $method.plot.blend.by_col,
@@ -501,6 +615,8 @@
                 <option value="VariableFeaturePlot">Plot Variable Genes with 'VariableFeaturePlot'</option>
                 <option value="VizDimLoadings">Visualize Reduction Results with 'VizDimLoadings'</option>
                 <option value="DimPlot">Visualize Dimensional Reduction with 'DimPlot'</option>
+                <option value="ImageDimPlot">Visualize spatial clusters or other categorical groupings with 'ImageDimPlot'</option>
+                <option value="ImageFeaturePlot">Visualize expression in a spatial context with 'ImageFeaturePlot'</option>
                 <option value="DimHeatmap">Visualize Reduction Results with 'DimHeatmap'</option>
                 <option value="ElbowPlot">Determine dimensionality with 'ElbowPlot'</option>
                 <option value="FeaturePlot">Visualize expression with 'FeaturePlot'</option>
@@ -687,19 +803,75 @@
                         <when value="false">
                         </when>
                     </conditional>
-                    <param name="na_value" type="select" label="Colour for NA points when using custom scale" help="(na.value)">
-                        <option value="lightgrey" selected="true">lightgrey</option>
-                        <option value="grey">grey</option>
-                        <option value="black">black</option>
-                    </param>
+                    <expand macro="plot_na_value"/>
                 </section>
                 <section name="adv" title="Advanced Options">
-                    <param argument="cells" type="data" format="txt,tabular" optional="true" label="List of cells to include on plot" help="text file with one cell on each line"/>
+                    <expand macro="plot_cells"/>
                     <expand macro="plot_group_by"/>
                     <expand macro="plot_split_by"/>
                     <param name="shape_by" type="text" optional="true" value="" label="Shape points by a group or identity" help="only when not saving as raster (shape.by)"/>
                 </section>
             </when>
+            <when value="ImageDimPlot">
+                <section name="plot" title="Plot Formatting Options">
+                    <expand macro="plot_fov"/>
+                    <expand macro="plot_boundaries"/>
+                    <expand macro="plot_cols"/>
+                    <expand macro="plot_shuffle_cols"/>
+                    <param name="size" type="float" value="1.0" label="Point size for cells" help="(size)"/>
+                    <expand macro="plot_alpha"/>
+                    <expand macro="plot_molecules"/>
+                    <expand macro="plot_mol_alpha"/>
+                    <expand macro="plot_nmols"/>
+                    <expand macro="plot_na_value"/>
+                </section>
+                <section name="adv" title="Advanced Options">
+                    <expand macro="plot_group_by"/>
+                    <expand macro="plot_split_by"/>
+                    <expand macro="plot_border"/>
+                    <expand macro="plot_dark_background"/>
+                    <expand macro="plot_crop"/>
+                    <expand macro="plot_cells"/>
+                    <expand macro="plot_overlap"/>
+                    <expand macro="plot_axes"/>
+                    <expand macro="plot_combine"/>
+                    <expand macro="plot_coord_fixed"/>
+                    <expand macro="plot_flip_xy"/>
+                </section>
+            </when>
+            <when value="ImageFeaturePlot">
+                <param argument="features" type="text" value="nFeature_RNA" label="Features to plot" help="comma-separated list e.g. MS4A1, percent.mito, PC_1"/>
+                <section name="plot" title="Plot Formatting Options">
+                    <expand macro="plot_fov"/>
+                    <expand macro="plot_boundaries"/>
+                    <param name="size" type="float" value="1.0" label="Point size for cells" help="(size)"/>
+                    <expand macro="plot_alpha"/>
+                    <expand macro="plot_molecules"/>
+                    <expand macro="plot_nmols"/>
+                    <param argument="blend" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Scale and blend expression values to visualize coexpression"/>
+                    <param name="blend_threshold" type="float" value="0.5" min="0" max="1" label="Colour cutoff from weak signal to strong signal" help="(blend.threshold)"/>
+                    <param name="scale" type="select" label="How to handle colour scale across multiple plots" help="(scale)">
+                        <option value="feature" selected="true">Scale each feature separately</option>
+                        <option value="all">Scale all to same maximum</option>
+                        <option value="none">Plots are not scaled</option>
+                    </param>
+                    <expand macro="raster_select"/>
+                </section>
+                <section name="adv" title="Advanced Options">
+                    <expand macro="plot_group_by"/>
+                    <expand macro="plot_split_by"/>
+                    <expand macro="plot_border"/>
+                    <expand macro="plot_dark_background"/>
+                    <expand macro="plot_crop"/>
+                    <expand macro="plot_cells"/>
+                    <expand macro="plot_coord_fixed"/>
+                    <expand macro="plot_overlap"/>
+                    <expand macro="plot_axes"/>
+                    <expand macro="plot_combine"/>
+                    <param name="min_cutoff" type="text" optional="true" value="" label="Minimum cutoff for features - as quantile" help="Minimum values for each feature eg, 'q1'or 'q10')"/>
+                    <param name="max_cutoff" type="text" optional="true" value="" label="Maximum cutoff for features - as quantile" help="Maximum values for each feature (eg, 'q1'or 'q10')"/>
+                </section>
+            </when>
             <when value="DimHeatmap">
                 <param argument="dims" type="text" value="1:10" label="Dimensions from reduction to plot" help="enter one or a range of dimensions e.g. 3 to plot dim 3, 1:10 to plot dims 1 to 10">
                     <validator type="regex" message="Please only use numbers or colon">^[\d:]+$</validator>
@@ -927,11 +1099,11 @@
                     <has_text_matching expression="VlnPlot"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/VlnPlot.png" ftype="png" compare="image_diff"/>
+            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/VlnPlot.png" ftype="png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test2: FeatureScatter PDF -->
-            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/filtered.rds"/>
+            <param name="seurat_rds" location="https://zenodo.org/records/17817806/files/filtered.rds"/>
             <param name="plot_format" value="png"/>
             <conditional name="method">
                 <param name="method" value="FeatureScatter"/>
@@ -946,11 +1118,11 @@
                     <has_text_matching expression="FeatureScatter"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/FeatureScatter.png" ftype="png" compare="image_diff"/>
+            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/FeatureScatter.png" ftype="png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test3: CellScatter PDF -->
-            <param name="seurat_rds" location="https://zenodo.org/records/13732784/files/variablefeatures.rds"/>
+            <param name="seurat_rds" location="https://zenodo.org/records/17817806/files/variablefeatures.rds"/>
             <param name="plot_format" value="pdf"/>
             <conditional name="method">
                 <param name="method" value="CellScatter"/>
@@ -967,7 +1139,7 @@
                     <has_text_matching expression="CellScatter"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_pdf" location="https://zenodo.org/records/13732784/files/CellScatter.pdf" ftype="pdf" compare="diff" lines_diff="50"/>
+            <output name="plot_out_pdf" location="https://zenodo.org/records/17817806/files/CellScatter.pdf" ftype="pdf" compare="diff" lines_diff="50"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test4: VariableFeaturePlot SVG -->
@@ -988,7 +1160,7 @@
                     <has_text_matching expression="VariableFeaturePlot"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_svg" location="https://zenodo.org/records/13732784/files/VariableFeaturePlot.svg" ftype="svg" compare="diff" lines_diff="50"/>
+            <output name="plot_out_svg" location="https://zenodo.org/records/17817806/files/VariableFeaturePlot.svg" ftype="svg" compare="diff" lines_diff="50"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test5: VizDimLoadings JPEG -->
@@ -1013,7 +1185,7 @@
                     <has_text_matching expression="VizDimLoadings"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_jpeg" location="https://zenodo.org/records/13732784/files/VizDimLoadings.jpeg" ftype="jpeg" compare="image_diff"/>
+            <output name="plot_out_jpeg" location="https://zenodo.org/records/17817806/files/VizDimLoadings.jpeg" ftype="jpeg" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test6: DimPlot TEX -->
@@ -1032,7 +1204,7 @@
                     <has_text_matching expression="DimPlot"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_tex" location="https://zenodo.org/records/13732784/files/DimPlot.tex" ftype="tex">
+            <output name="plot_out_tex" location="https://zenodo.org/records/17817806/files/DimPlot.tex" ftype="tex">
                 <assert_contents>
                     <has_text_matching expression="beginpicture"/>
                 </assert_contents>
@@ -1065,7 +1237,7 @@
                     <has_text_matching expression="DimHeatmap"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_tiff" location="https://zenodo.org/records/13732784/files/DimHeatmap.tiff" ftype="tiff" compare="image_diff"/>
+            <output name="plot_out_tiff" location="https://zenodo.org/records/17817806/files/DimHeatmap.tiff" ftype="tiff" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test8: ElbowPlot EPS -->
@@ -1084,7 +1256,7 @@
                     <has_text_matching expression="ElbowPlot"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_eps" location="https://zenodo.org/records/13732784/files/ElbowPlot.eps" ftype="eps"/>
+            <output name="plot_out_eps" location="https://zenodo.org/records/17817806/files/ElbowPlot.eps" ftype="eps"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test9: FeaturePlot PNG -->
@@ -1108,7 +1280,7 @@
                     <has_text_matching expression="FeaturePlot"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/FeaturePlot.png" ftype="png" compare="image_diff"/>
+            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/FeaturePlot.png" ftype="png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test10: DoHeatmap PNG -->
@@ -1136,7 +1308,7 @@
                     <has_text_matching expression="DoHeatmap"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/DoHeatmap.png" ftype="png" compare="image_diff"/>
+            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/DoHeatmap.png" ftype="png" compare="image_diff"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test11: DotPlot PNG -->
@@ -1154,7 +1326,44 @@
                     <has_text_matching expression="DotPlot"/>
                 </assert_contents>
             </output>
-            <output name="plot_out_png" location="https://zenodo.org/records/13732784/files/DotPlot.png" ftype="png" compare="image_diff"/>
+            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/DotPlot.png" ftype="png" compare="image_diff"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test12: ImageDimPlot PNG -->
+            <param name="seurat_rds" location="https://zenodo.org/records/17807529/files/test_seurat_spatial.rds"/>
+            <param name="plot_format" value="png"/>
+            <conditional name="method">
+                <param name="fov" value="anterior1"/>
+                <param name="method" value="ImageDimPlot"/>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="ImageDimPlot"/>
+                </assert_contents>
+            </output>
+            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/ImageDimPlot.png" ftype="png" compare="image_diff"/>
+        </test>
+        <test expect_num_outputs="2">
+            <!-- test13: ImageFeaturePlot PNG -->
+            <param name="seurat_rds" location="https://zenodo.org/records/17807529/files/test_seurat_spatial.rds"/>
+            <param name="plot_format" value="png"/>
+            <conditional name="method">
+                <param name="method" value="ImageFeaturePlot"/>
+                <param name="fov" value="anterior1"/>
+                <param name="features" value="Xkr4"/>
+            </conditional>
+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="hidden_output">
+                <assert_contents>
+                    <has_text_matching expression="ImageFeaturePlot"/>
+                </assert_contents>
+            </output>
+            <output name="plot_out_png" location="https://zenodo.org/records/17817806/files/ImageFeaturePlot.png" ftype="png" compare="image_diff"/>
         </test>
     </tests>
     <help><![CDATA[